I have same issue.
Running zcs-3.1.2_GA_445.FC4 on FC4 ( Fedora Core 4 ).
Tried both as zimbra user and as root doing via sudo -u zimbra .
Same thing.
Followed WIKI instructions to the letter.
After each error, I started with new "instance" ( running via VMware so just recopied each time ).

No other issues with Zimbra really. Just wanted to push the cert expiry date out further.
The current cert will expire 9/11/06.